LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -45.114701 0.0000000) to (15.038234 45.114701 3.6473074) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4230099 4.4230099 3.6473074 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -45.114701 0.0000000) to (15.038234 45.114701 3.6473074) create_atoms CPU = 0.002 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4230099 4.4230099 3.6473074 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -45.114701 0.0000000) to (15.038234 45.114701 3.6473074) create_atoms CPU = 0.001 seconds 206 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 34 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 408 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_608695023236_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.825 | 4.825 | 4.825 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1573.9749 0 -1573.9749 64672.995 49 0 -1684.978 0 -1684.978 7880.7604 Loop time of 5.22367 on 1 procs for 49 steps with 408 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1573.97491739624 -1684.97652137175 -1684.97804280121 Force two-norm initial, final = 287.15793 0.13944272 Force max component initial, final = 73.055908 0.014096828 Final line search alpha, max atom move = 1.0000000 0.014096828 Iterations, force evaluations = 49 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2111 | 5.2111 | 5.2111 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0063069 | 0.0063069 | 0.0063069 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006277 | | | 0.12 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2772.00 ave 2772 max 2772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21976.0 ave 21976 max 21976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21976 Ave neighs/atom = 53.862745 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.825 | 4.825 | 4.825 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -1684.978 0 -1684.978 7880.7604 4948.9979 53 0 -1685.0445 0 -1685.0445 256.51934 4971.4361 Loop time of 0.332962 on 1 procs for 4 steps with 408 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1684.97804280121 -1685.04411987793 -1685.04445600476 Force two-norm initial, final = 42.944456 1.4506379 Force max component initial, final = 29.392967 1.0903268 Final line search alpha, max atom move = 0.00072889168 0.00079473011 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33125 | 0.33125 | 0.33125 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037176 | 0.00037176 | 0.00037176 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001337 | | | 0.40 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2724.00 ave 2724 max 2724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21864.0 ave 21864 max 21864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21864 Ave neighs/atom = 53.588235 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.963 | 4.963 | 4.963 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1685.0445 0 -1685.0445 256.51934 Loop time of 6.095e-06 on 1 procs for 0 steps with 408 atoms 180.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.095e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2724.00 ave 2724 max 2724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21864.0 ave 21864 max 21864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21864 Ave neighs/atom = 53.588235 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.963 | 4.963 | 4.963 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -1685.0445 -1685.0445 15.032334 90.471038 3.6554924 256.51934 256.51934 179.51552 237.86736 352.17514 2.337832 118.44705 Loop time of 7.317e-06 on 1 procs for 0 steps with 408 atoms 232.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.317e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2724.00 ave 2724 max 2724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10932.0 ave 10932 max 10932 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21864.0 ave 21864 max 21864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21864 Ave neighs/atom = 53.588235 Neighbor list builds = 0 Dangerous builds = 0 408 -1685.04445600476 eV 2.33783195807769 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06